| """Molecular data structures.""" |
|
|
| from functools import partial |
| from pathlib import Path |
| from typing import Any, Iterable, Optional |
| from haddock.libs.libontology import PDBFile |
|
|
|
|
| class Molecule: |
| """ |
| Input molecule, usually a PDB file. |
| |
| Parameters |
| ---------- |
| file_name : :external:py:class:`pathlib.Path` |
| The path to the molecule file. |
| |
| segid : int, optional |
| The ID of the segment. Defaults to ``None``. |
| |
| no_parent : boolean |
| Whether to add the parent path ``..`` to the |
| :py:attr:`haddock.libs.libstructure.Molecule.with_parent`. |
| When set to true, the ``with_parent`` attribute returns the same |
| as ``file_name``. |
| """ |
|
|
| def __init__( |
| self, file_name: Path, segid: Optional[int] = None, no_parent: bool = False |
| ) -> None: |
| |
| assert isinstance(file_name, Path), ( |
| f"`file_name` must be pathlib.Path: {type(file_name)} given" |
| ) |
|
|
| self.file_name = file_name |
| self.segid = segid |
| if no_parent: |
| self.with_parent = file_name |
| else: |
| self.with_parent = Path("..", file_name) |
|
|
|
|
| def make_molecules(paths: Iterable[Path], **kwargs: Any) -> list[Molecule]: |
| """Get input molecules from the data stream.""" |
| return list(map(partial(Molecule, **kwargs), paths)) |
|
|
|
|
| def find_ff(models: list[PDBFile]) -> str: |
| """Finds the force-field information (all-atom or martini) from the topology |
| associated to the first model. Used in caprieval and caprifilter. |
| |
| The assumption is that the force-fields will be identical between models. |
| |
| Parameters |
| ----------- |
| models : list[PDBFile] |
| List of models where to find the topology |
| |
| Return |
| ------- |
| ff : str |
| The force-field used in those models. |
| """ |
| try: |
| ff = Path(models[0].topology[0].rel_path).stem.split("_")[-1] |
| except TypeError: |
| try: |
| ff = Path(models[0].topology.rel_path).stem.split("_")[-1] |
| except AttributeError: |
| ff = "aa" |
| |
| if "martini" not in ff: |
| ff = "aa" |
|
|
| return ff |
|
|
